Difference between revisions of "Team:Jilin China/Part Collection"
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<div> | <div> | ||
<h2>Abstract</h2> | <h2>Abstract</h2> | ||
| − | <p>This year, Jilin_China made a RNA-based thermosensor toolkit for users, | + | <p>This year, Jilin_China made a RNA-based thermosensor toolkit for users, which includes four types of RNA-based thermosensors: heat-inducible, heat-repressible, cold-inducible and cold-repressible RNA-based thermosensors. But due to the numbers of cold-inducible RNA-based thermosensors is less than 10, which can't meet the number requirement(more than 10) of collection, we added three types of collections to the parts registry as follows:</p> |
| − | <p> | + | <p><b>heat-inducible RNA-based thermosensor collection</b>, <b>heat-repressible RNA-based thermosensor collection</b> and <b>cold-repressible RNA-based thermosensor collection</b>.</p> |
<p>In order to make it easier for users to select an appropriate RNA-based thermosensor, we also developed a search engine for our toolkit, you can click here to enter the search engine page.</p> | <p>In order to make it easier for users to select an appropriate RNA-based thermosensor, we also developed a search engine for our toolkit, you can click here to enter the search engine page.</p> | ||
| − | <p>The introduction of each type of part collection is as | + | <p>The introduction of each type of part collection is as follows: </p> |
</div> | </div> | ||
</li> | </li> | ||
| Line 102: | Line 102: | ||
<div> | <div> | ||
<h2>Heat-inducible RNA-based thermosensor collection</h2> | <h2>Heat-inducible RNA-based thermosensor collection</h2> | ||
| − | <p>In this collection, we provide a total of 48 different RNA-based thermosensors, which can regulate the expression of genes with the changed temperature | + | <p>In this collection, we provide a total of 48 different Heat-inducible RNA-based thermosensors, which can regulate the expression of genes with the changed temperature. The RNA-based thermosensors we designed has been characterized and mathematically fitted to prove that they have different melting temperature, expression intensity and sensitivity. Users can choose the appropriate RNA-based thermosensors according to their own needs.</p> |
<p>Heat-inducible RNA-based thermosensor collection contains these parts:</p> | <p>Heat-inducible RNA-based thermosensor collection contains these parts:</p> | ||
<div class="collection"><table width="auto"> | <div class="collection"><table width="auto"> | ||
| Line 162: | Line 162: | ||
<div> | <div> | ||
<h2>Heat-repressible RNA-based thermosensor collection</h2> | <h2>Heat-repressible RNA-based thermosensor collection</h2> | ||
| − | <p>In order to make our RNA-based thermosensor toolkit more suitable for users' needs, we updated the toolkit to version 2.0. We added the RNase E-based heat-repressible RNA-based thermosensors, including 23 different thermosensors. The stem-loop structure of the thermosensor contains the | + | <p>In order to make our RNA-based thermosensor toolkit more suitable for users' needs, we updated the toolkit to version 2.0. We added the RNase E-based heat-repressible RNA-based thermosensors, including 23 different thermosensors. The stem-loop structure of the thermosensor contains the RNase E cleavage site. At the elevated temperature, the cleavage site is exposed, and the mRNA will be degraded, which turns the translation off. </p> |
<p>Heat-repressible RNA-based thermosensor collection contain these parts:</p> | <p>Heat-repressible RNA-based thermosensor collection contain these parts:</p> | ||
<div class="collection"><table width="auto"> | <div class="collection"><table width="auto"> | ||
| Line 172: | Line 172: | ||
<tr><td>Heat-repressible RNA-based thermosensor-5</td><td>BBa_K2541105</td></tr> | <tr><td>Heat-repressible RNA-based thermosensor-5</td><td>BBa_K2541105</td></tr> | ||
<tr><td>Heat-repressible RNA-based thermosensor-6</td><td>BBa_K2541106</td></tr> | <tr><td>Heat-repressible RNA-based thermosensor-6</td><td>BBa_K2541106</td></tr> | ||
| − | |||
<tr><td>Heat-repressible RNA-based thermosensor-8</td><td>BBa_K2541108</td></tr> | <tr><td>Heat-repressible RNA-based thermosensor-8</td><td>BBa_K2541108</td></tr> | ||
<tr><td>Heat-repressible RNA-based thermosensor-9</td><td>BBa_K2541109</td></tr> | <tr><td>Heat-repressible RNA-based thermosensor-9</td><td>BBa_K2541109</td></tr> | ||
| Line 191: | Line 190: | ||
</table></div> | </table></div> | ||
| − | <p>For more detailed principles of Heat- | + | <p>For more detailed principles of Heat-repressible RNA-based thermosensors, you can read our design page.</p> |
<center><a href="https://2018.igem.org/Team:Jilin_China/Design">>Click here to read the design of the Heat-repressible RNA-based thermosensors!<</a></center> | <center><a href="https://2018.igem.org/Team:Jilin_China/Design">>Click here to read the design of the Heat-repressible RNA-based thermosensors!<</a></center> | ||
| Line 199: | Line 198: | ||
<div> | <div> | ||
<h2>Cold-inducible RNA-based thermosensor collection</h2> | <h2>Cold-inducible RNA-based thermosensor collection</h2> | ||
| − | <p> | + | <p>To expand the melting temprerature range of the thermosenor, we have made a second upgrade to the toolkit. In toolkit 3.0, we added cold-repressible and cold-inducible RNA thermosenor, and made 8 cold-inducible RNA-based thermosensors into the part collection.</p> |
<p>Cold-inducible RNA-based thermosensor collection contains these parts:</p> | <p>Cold-inducible RNA-based thermosensor collection contains these parts:</p> | ||
<div class="collection"><table width="auto"> | <div class="collection"><table width="auto"> | ||
| Line 218: | Line 217: | ||
<div> | <div> | ||
<h2>Cold-repressible RNA-based thermosensor collection</h2> | <h2>Cold-repressible RNA-based thermosensor collection</h2> | ||
| − | <p>To expand the melting temprerature range of the thermosenor, we have made a second upgrade to the toolkit. In toolkit 3.0, we added cold-repressible and cold inducible RNA thermosenor, and made 10 cold-repressible RNA-based thermosensors into a part collection.</p> | + | <p>To expand the melting temprerature range of the thermosenor, we have made a second upgrade to the toolkit. In toolkit 3.0, we added cold-repressible and cold-inducible RNA thermosenor, and made 10 cold-repressible RNA-based thermosensors into a part collection.</p> |
| − | <p>Cold-repressible RNA-based thermosensor is based | + | <p>Cold-repressible RNA-based thermosensor is based on the RNase III. The stem-loop of the thermosensor mRNA contains the recognition and cleavage site of RNase III. When the temperature is lower than the melting temperature, the RNase III will degrade the mRNA.</p> |
<p>Cold-repressible RNA-based thermosensor collection contain these parts:</p> | <p>Cold-repressible RNA-based thermosensor collection contain these parts:</p> | ||
<div class="collection"><table width="200" border="1"> | <div class="collection"><table width="200" border="1"> | ||
| Line 236: | Line 235: | ||
</tbody> | </tbody> | ||
</table></div> | </table></div> | ||
| − | <p>For more detailed principles of | + | <p>For more detailed principles of Cold-repressible RNA-based thermosensors, you can read our design page.</p> |
<center><a href="https://2018.igem.org/Team:Jilin_China/Design">>Click here to read the design of the Cold-repressible RNA-based thermosensors!<</a></center> | <center><a href="https://2018.igem.org/Team:Jilin_China/Design">>Click here to read the design of the Cold-repressible RNA-based thermosensors!<</a></center> | ||
| Line 243: | Line 242: | ||
<li class="paragraph_6" id="paragraph_6"> | <li class="paragraph_6" id="paragraph_6"> | ||
<div> | <div> | ||
| − | <h2> | + | <h2>References</h2> |
| − | + | <ul> | |
| + | <li>[1] Sen S, Apurva D, Satija R, et al. Design of a Toolbox of RNA Thermometers[J]. Acs Synthetic Biology, 2017, 6(8).</li> | ||
| + | <li>[2] Hoynes-O’Connor, A., Hinman, K., Kirchner, L., and Moon, T.S. (2015) De novo design | ||
| + | of heat-repressible RNA thermosensors in E.coli. Nucleic Acids Res. 43, 6166−6179.</li> | ||
| + | <li>[3] Pertzev A V, Nicholson A W. Characterization of RNA sequence determinants and antideterminants of processing reactivity for a minimal substrate of Escherichia coli ribonuclease III[J]. Nucleic Acids Research, 2006, 34(13):3708-3721.</li> | ||
| + | <li>[4] Giuliodori A M, Pietro F D, Marzi S, et al. The cspA, mRNA Is a Thermosensor that Modulates Translation of the Cold-Shock Protein CspA[J]. Molecular Cell, 2010, 37(1):21-33.</li> | ||
| + | <li>[5] Engler C, Kandzia R, Marillonnet S. A one pot, one step, precision cloning method with high throughput capability[J]. Plos One, 2008, 3(11):e3647.</li> | ||
| + | </ul> | ||
</div> | </div> | ||
</li> | </li> | ||
Latest revision as of 21:58, 17 October 2018
PART
COLLECTION
Part Collection
-
Abstract
This year, Jilin_China made a RNA-based thermosensor toolkit for users, which includes four types of RNA-based thermosensors: heat-inducible, heat-repressible, cold-inducible and cold-repressible RNA-based thermosensors. But due to the numbers of cold-inducible RNA-based thermosensors is less than 10, which can't meet the number requirement(more than 10) of collection, we added three types of collections to the parts registry as follows:
heat-inducible RNA-based thermosensor collection, heat-repressible RNA-based thermosensor collection and cold-repressible RNA-based thermosensor collection.
In order to make it easier for users to select an appropriate RNA-based thermosensor, we also developed a search engine for our toolkit, you can click here to enter the search engine page.
The introduction of each type of part collection is as follows:
-
Heat-inducible RNA-based thermosensor collection
In this collection, we provide a total of 48 different Heat-inducible RNA-based thermosensors, which can regulate the expression of genes with the changed temperature. The RNA-based thermosensors we designed has been characterized and mathematically fitted to prove that they have different melting temperature, expression intensity and sensitivity. Users can choose the appropriate RNA-based thermosensors according to their own needs.
Heat-inducible RNA-based thermosensor collection contains these parts:
Part Name Part Number Heat-inducible RNA-based thermosensor-1 BBa_K2541001 Heat-inducible RNA-based thermosensor-2 BBa_K2541002 Heat-inducible RNA-based thermosensor-3 BBa_K2541003 Heat-inducible RNA-based thermosensor-4 BBa_K2541004 Heat-inducible RNA-based thermosensor-5 BBa_K2541005 Heat-inducible RNA-based thermosensor-6 BBa_K2541006 Heat-inducible RNA-based thermosensor-7 BBa_K2541007 Heat-inducible RNA-based thermosensor-8 BBa_K2541008 Heat-inducible RNA-based thermosensor-9 BBa_K2541009 Heat-inducible RNA-based thermosensor-10 BBa_K2541010 Heat-inducible RNA-based thermosensor-11 BBa_K2541011 Heat-inducible RNA-based thermosensor-12 BBa_K2541012 Heat-inducible RNA-based thermosensor-13 BBa_K2541013 Heat-inducible RNA-based thermosensor-14 BBa_K2541014 Heat-inducible RNA-based thermosensor-15 BBa_K2541015 Heat-inducible RNA-based thermosensor-16 BBa_K2541016 Heat-inducible RNA-based thermosensor-17 BBa_K2541017 Heat-inducible RNA-based thermosensor-18 BBa_K2541018 Heat-inducible RNA-based thermosensor-19 BBa_K2541019 Heat-inducible RNA-based thermosensor-20 BBa_K2541020 Heat-inducible RNA-based thermosensor-21 BBa_K2541021 Heat-inducible RNA-based thermosensor-25 BBa_K2541025 Heat-inducible RNA-based thermosensor-26 BBa_K2541026 Heat-inducible RNA-based thermosensor-27 BBa_K2541027 Heat-inducible RNA-based thermosensor-28 BBa_K2541028 Heat-inducible RNA-based thermosensor-29 BBa_K2541029 Heat-inducible RNA-based thermosensor-30 BBa_K2541030 Heat-inducible RNA-based thermosensor-31 BBa_K2541031 Heat-inducible RNA-based thermosensor-32 BBa_K2541032 Heat-inducible RNA-based thermosensor-33 BBa_K2541033 Heat-inducible RNA-based thermosensor-34 BBa_K2541034 Heat-inducible RNA-based thermosensor-35 BBa_K2541035 Heat-inducible RNA-based thermosensor-36 BBa_K2541036 Heat-inducible RNA-based thermosensor-37 BBa_K2541037 Heat-inducible RNA-based thermosensor-38 BBa_K2541038 Heat-inducible RNA-based thermosensor-39 BBa_K2541039 Heat-inducible RNA-based thermosensor-40 BBa_K2541040 Heat-inducible RNA-based thermosensor-41 BBa_K2541041 Heat-inducible RNA-based thermosensor-42 BBa_K2541042 Heat-inducible RNA-based thermosensor-43 BBa_K2541043 Heat-inducible RNA-based thermosensor-44 BBa_K2541044 Heat-inducible RNA-based thermosensor-45 BBa_K2541045 Heat-inducible RNA-based thermosensor-46 BBa_K2541046 Heat-inducible RNA-based thermosensor-47 BBa_K2541047 Heat-inducible RNA-based thermosensor-48 BBa_K2541048 Heat-inducible RNA-based thermosensor-49 BBa_K2541049 Heat-inducible RNA-based thermosensor-50 BBa_K2541050 Heat-inducible RNA-based thermosensor-51 BBa_K2541051 Heat-inducible RNA-based thermosensor collection can cover melting temperature from 33 to 55 degrees with different intensity and sensitivity.
For more detailed principles of Heat-inducible RNA-based thermosensors, you can read our design page.
>Click here to read the design of the Heat-inducible RNA-based thermosensors!< Heat-repressible RNA-based thermosensor collection
In order to make our RNA-based thermosensor toolkit more suitable for users' needs, we updated the toolkit to version 2.0. We added the RNase E-based heat-repressible RNA-based thermosensors, including 23 different thermosensors. The stem-loop structure of the thermosensor contains the RNase E cleavage site. At the elevated temperature, the cleavage site is exposed, and the mRNA will be degraded, which turns the translation off.
Heat-repressible RNA-based thermosensor collection contain these parts:
Part Name Part Number Heat-repressible RNA-based thermosensor-1 BBa_K2541101 Heat-repressible RNA-based thermosensor-2 BBa_K2541102 Heat-repressible RNA-based thermosensor-3 BBa_K2541103 Heat-repressible RNA-based thermosensor-4 BBa_K2541104 Heat-repressible RNA-based thermosensor-5 BBa_K2541105 Heat-repressible RNA-based thermosensor-6 BBa_K2541106 Heat-repressible RNA-based thermosensor-8 BBa_K2541108 Heat-repressible RNA-based thermosensor-9 BBa_K2541109 Heat-repressible RNA-based thermosensor-10 BBa_K2541110 Heat-repressible RNA-based thermosensor-11 BBa_K2541111 Heat-repressible RNA-based thermosensor-12 BBa_K2541112 Heat-repressible RNA-based thermosensor-13 BBa_K2541113 Heat-repressible RNA-based thermosensor-14 BBa_K2541114 Heat-repressible RNA-based thermosensor-15 BBa_K2541115 Heat-repressible RNA-based thermosensor-16 BBa_K2541116 Heat-repressible RNA-based thermosensor-17 BBa_K2541117 Heat-repressible RNA-based thermosensor-18 BBa_K2541118 Heat-repressible RNA-based thermosensor-19 BBa_K2541119 Heat-repressible RNA-based thermosensor-20 BBa_K2541120 Heat-repressible RNA-based thermosensor-21 BBa_K2541121 Heat-repressible RNA-based thermosensor-22 BBa_K2541122 Heat-repressible RNA-based thermosensor-23 BBa_K2541123 For more detailed principles of Heat-repressible RNA-based thermosensors, you can read our design page.
>Click here to read the design of the Heat-repressible RNA-based thermosensors!< Cold-inducible RNA-based thermosensor collection
To expand the melting temprerature range of the thermosenor, we have made a second upgrade to the toolkit. In toolkit 3.0, we added cold-repressible and cold-inducible RNA thermosenor, and made 8 cold-inducible RNA-based thermosensors into the part collection.
Cold-inducible RNA-based thermosensor collection contains these parts:
Part Name Part Number Cold-inducible RNA-based thermosensor-1 BBa_K2541301 Cold-inducible RNA-based thermosensor-2 BBa_K2541302 Cold-inducible RNA-based thermosensor-3 BBa_K2541303 Cold-inducible RNA-based thermosensor-4 BBa_K2541304 Cold-inducible RNA-based thermosensor-5 BBa_K2541305 Cold-inducible RNA-based thermosensor-6 BBa_K2541306 Cold-inducible RNA-based thermosensor-7 BBa_K2541307 Cold-inducible RNA-based thermosensor-8 BBa_K2541308 For more detailed principles of Cold-inducible RNA-based thermosensors, you can read our design page.
>Click here to read the design of the Cold-inducible RNA-based thermosensors!< Cold-repressible RNA-based thermosensor collection
To expand the melting temprerature range of the thermosenor, we have made a second upgrade to the toolkit. In toolkit 3.0, we added cold-repressible and cold-inducible RNA thermosenor, and made 10 cold-repressible RNA-based thermosensors into a part collection.
Cold-repressible RNA-based thermosensor is based on the RNase III. The stem-loop of the thermosensor mRNA contains the recognition and cleavage site of RNase III. When the temperature is lower than the melting temperature, the RNase III will degrade the mRNA.
Cold-repressible RNA-based thermosensor collection contain these parts:
Part Name Part Number Cold-repressible RNA-based thermosensor-1 BBa_K2541201 Cold-repressible RNA-based thermosensor-2 BBa_K2541202 Cold-repressible RNA-based thermosensor-3 BBa_K2541203 Cold-repressible RNA-based thermosensor-4 BBa_K2541204 Cold-repressible RNA-based thermosensor-5 BBa_K2541205 Cold-repressible RNA-based thermosensor-6 BBa_K2541206 Cold-repressible RNA-based thermosensor-7 BBa_K2541207 Cold-repressible RNA-based thermosensor-8 BBa_K2541208 Cold-repressible RNA-based thermosensor-9 BBa_K2541209 Cold-repressible RNA-based thermosensor-10 BBa_K2541210 For more detailed principles of Cold-repressible RNA-based thermosensors, you can read our design page.
>Click here to read the design of the Cold-repressible RNA-based thermosensors!< References
- [1] Sen S, Apurva D, Satija R, et al. Design of a Toolbox of RNA Thermometers[J]. Acs Synthetic Biology, 2017, 6(8).
- [2] Hoynes-O’Connor, A., Hinman, K., Kirchner, L., and Moon, T.S. (2015) De novo design of heat-repressible RNA thermosensors in E.coli. Nucleic Acids Res. 43, 6166−6179.
- [3] Pertzev A V, Nicholson A W. Characterization of RNA sequence determinants and antideterminants of processing reactivity for a minimal substrate of Escherichia coli ribonuclease III[J]. Nucleic Acids Research, 2006, 34(13):3708-3721.
- [4] Giuliodori A M, Pietro F D, Marzi S, et al. The cspA, mRNA Is a Thermosensor that Modulates Translation of the Cold-Shock Protein CspA[J]. Molecular Cell, 2010, 37(1):21-33.
- [5] Engler C, Kandzia R, Marillonnet S. A one pot, one step, precision cloning method with high throughput capability[J]. Plos One, 2008, 3(11):e3647.